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- PDB-1mk9: CRYSTAL STRUCTURE OF AN INTEGRIN BETA3-TALIN CHIMERA -

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Basic information

Entry
Database: PDB / ID: 1mk9
TitleCRYSTAL STRUCTURE OF AN INTEGRIN BETA3-TALIN CHIMERA
Components
  • Integrin Beta3
  • TALIN
KeywordsSTRUCTURAL PROTEIN / FOCAL ADHESION / INTEGRIN BINDING / FERM DOMAIN / CYTOSKELETON NPXY MOTIF / PTB DOMAIN
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / positive regulation of bone resorption / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / glycinergic synapse / regulation of release of sequestered calcium ion into cytosol / filopodium membrane / extracellular matrix binding / wound healing, spreading of epidermal cells / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / positive regulation of smooth muscle cell migration / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / cell adhesion mediated by integrin / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / cellular response to insulin-like growth factor stimulus / protein disulfide isomerase activity / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of osteoblast proliferation / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / blood coagulation, fibrin clot formation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / cellular response to platelet-derived growth factor stimulus / ruffle / positive regulation of endothelial cell proliferation / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / substrate adhesion-dependent cell spreading / embryo implantation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / cell-matrix adhesion / response to activity / integrin-mediated signaling pathway / Signal transduction by L1 / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / cell-cell adhesion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / structural constituent of cytoskeleton / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / cellular response to xenobiotic stimulus / ruffle membrane / positive regulation of fibroblast proliferation
Similarity search - Function
Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain ...Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / Acyl-CoA Binding Protein - #10 / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Acyl-CoA Binding Protein / Alpha-catenin/vinculin-like superfamily / : / : / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / FERM domain signature 2. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Integrin beta-3 / Talin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGarcia-Alvarez, B. / De Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural Determinants of Integrin Recognition by Talin
Authors: Garcia-Alvarez, B. / de Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE DATABASE. THE SEQUENCE HAS BEEN DESCRIBED IN THE PUBLICATION: HEMMINGS, L., REES, D.J.G., OHANIAN, V., BOLTON, S.J., GILMORE, A.P., PATEL, N., PRIDDLE, H., TREVITHICK, J.E., HYNES, R.O., & CRITCHLEY, D.R. (1996). TALIN CONTAINS THREE ACTIN-BINDING SITES EACH OF WHICH IS ADJACENT TO A VINCULIN-BINDING SITE. J. CELL SCI., 109, 2715-2726.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin Beta3
B: TALIN
C: Integrin Beta3
D: TALIN
E: Integrin Beta3
F: TALIN
G: Integrin Beta3
H: TALIN


Theoretical massNumber of molelcules
Total (without water)95,9478
Polymers95,9478
Non-polymers00
Water55831
1
A: Integrin Beta3
D: TALIN


Theoretical massNumber of molelcules
Total (without water)23,9872
Polymers23,9872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area12180 Å2
MethodPISA
2
B: TALIN
C: Integrin Beta3


Theoretical massNumber of molelcules
Total (without water)23,9872
Polymers23,9872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
3
E: Integrin Beta3
H: TALIN


Theoretical massNumber of molelcules
Total (without water)23,9872
Polymers23,9872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-6 kcal/mol
Surface area12170 Å2
MethodPISA
4
F: TALIN
G: Integrin Beta3


Theoretical massNumber of molelcules
Total (without water)23,9872
Polymers23,9872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-5 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.257, 141.763, 59.597
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Integrin Beta3


Mass: 1835.990 Da / Num. of mol.: 4 / Fragment: PARTIAL CYTOPLASMIC TAIL (Residues 739-750)
Source method: isolated from a genetically manipulated source
Details: Forms chimera with talin at the C-terminus / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05106
#2: Protein
TALIN


Mass: 22150.656 Da / Num. of mol.: 4
Fragment: F2 AND F3 SUBDOMAINS OF FERM DOMAIN (Residues 209-400)
Source method: isolated from a genetically manipulated source
Details: Forms chimera with Integrin Beta3 at the N-terminus
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54939
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 8000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113.5 mg/mlprotein1drop
220 mMTris-HCl1droppH7.0
3150 mM1dropNaCl
42 mMdithiothreitol1drop
50.1 MTris-HCl1reservoirpH8.6
60.2 M1reservoirMgCl2
718-20 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→29.83 Å / Num. obs: 18904 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 3.11 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4 / % possible all: 94.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 57904 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.307

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4MOLREPmodel building
CNS1.1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIX

1mix


Resolution: 2.8→29.83 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1387 7.4 %RANDOM
Rwork0.242 ---
obs0.242 18821 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9626 Å2 / ksol: 0.315075 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å20 Å2-1.12 Å2
2--2.34 Å20 Å2
3----9.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 0 31 6640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 236 7.4 %
Rwork0.304 2961 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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